Humans can innately track a moving target by anticipating its future position from a brief history of observations. While ballistic trajectories can be readily extrapolated, many natural and artificial systems are governed by more general nonlinear dynamics and, therefore, can produce highly irregular motion. Yet, relatively little is known regarding the behavioral and physiological underpinnings of prediction and tracking in the presence of chaos. Here, we investigated in lab settings whether participants could manually follow the orbit of a paradigmatic chaotic system, the Rössler equations, on the (x,y) plane under different settings of a control parameter, which determined the prominence of transients in the target position. Tracking accuracy was negatively related to the level of unpredictability and folding. Nevertheless, while participants initially reacted to the transients, they gradually learned to anticipate it. This was accompanied by a decrease in muscular co-contraction, alongside enhanced activity in the theta and beta EEG bands for the highest levels of chaoticity. Furthermore, greater phase synchronization of breathing was observed. Taken together, these findings point to the possible ability of the nervous system to implicitly learn topological regularities even in the context of highly irregular motion, reflecting in multiple observables at the physiological level.